Amature slowing down after separating and recombining in a single Armature multiple times
Just figured it out.

It really was a Rigify issue. What happens is that it left out some junk Drivers and during the process of separating and recombining, it duplicated until there was too many and it slowed down the Armature.

The fix was to look at the drivers and well… delete them. It kinda took some time for me because simply clicking and showing the driver graph slowed Blender also.